Transcriptional Profiling of Geminivirus Infection in Arabidopsis thaliana Col-0

Abstract

Geminiviruses are small DNA viruses that replicate in the nucleus and use plant replication machinery to amplify their single-stranded genomes. Geminiviruses replicate through a combination of rolling-circle and recombination-dependent replication. Earlier studies showed that the geminivirus, Cabbage leaf curl virus (CaLCuV), induces transcription of a host gene encoding a replication factor. To scrutinize the global impact of geminivirus infection on host gene expression, Arabidopsis transcriptome in response to CaLCuV infection at 12 days post inoculation was examined. These experiments uncovered 5241 Arabidopsis genes with changes in transcript levels (q < 0.004, p < 0.002) in response to infection. Data mining of the differentially expressed genes revealed that CaLCuV triggers a pathogen response via the salicylic acid pathway and inhibits the jasmonate pathway. CaLCuV also induced genes associated with programmed cell death and genotoxic stress, including components of the host DNA repair apparatus. CaLCuV also impacted expression of cell cycle-associated genes, preferentially activating genes with peak expression in S and G2 and inhibiting genes that peak in G1 and M. A limited set of core cell cycle genes expressed during cell cycle re-entry, late G1, S and early G2 had increased RNA levels, while core cell cycle genes expressed in early G1 and late G2 had reduced transcript levels. FACS analysis of nuclei from infected leaves showed an increase in 8C, 16C and 32C DNA content relative to nuclei from control leaves. Together, these results underscore the complexity of geminivirus/host interactions and establish that geminiviruses alter cell cycle controls to induce plant cells to move into an endocycle and support viral replication. We also standardized a previously reported method for inoculating geminiviruses using plasmid DNA rubbed onto leaves in the presence of an abrasive (DNA abrasion). We can obtain 100% inoculation efficiency with this method in solanaceous plants. Silencing of an endogenous gene was successful when a silencing vector was inoculated by DNA abrasion.